Merge branch 'master' into rodRefactor

Conflicts:
	public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCF.java
	public/java/test/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreatorIntegrationTest.java
	public/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersIntegrationTest.java

public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java

@@ -240,6 +240,14 @@ public class VariantDataManager {
             if( jitter && annotationKey.equalsIgnoreCase("HRUN") ) { // Integer valued annotations must be jittered a bit to work in this GMM
                   value += -0.25 + 0.5 * GenomeAnalysisEngine.getRandomGenerator().nextDouble();
             }
+	    if (vc.isIndel() && annotationKey.equalsIgnoreCase("QD")) {
+		// normalize QD by event length for indel case
+		int eventLength = Math.abs(vc.getAlternateAllele(0).getBaseString().length() - vc.getReference().getBaseString().length()); // ignore multi-allelic complication here for now
+		    if (eventLength > 0) // sanity check
+			value /= (double)eventLength;
+
+	    }
+
             if( jitter && annotationKey.equalsIgnoreCase("HaplotypeScore") && MathUtils.compareDoubles(value, 0.0, 0.0001) == 0 ) { value = -0.2 + 0.4*GenomeAnalysisEngine.getRandomGenerator().nextDouble(); }
             if( jitter && annotationKey.equalsIgnoreCase("FS") && MathUtils.compareDoubles(value, 0.0, 0.001) == 0 ) { value = -0.2 + 0.4*GenomeAnalysisEngine.getRandomGenerator().nextDouble(); }
         } catch( Exception e ) {

public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariants.java

@@ -154,10 +154,10 @@ public class ValidateVariants extends RodWalker<Integer, Integer> {
         try {
             switch( type ) {
                 case ALL:
-                    vc.extraStrictValidation(observedRefAllele, rsIDs);
+                    vc.extraStrictValidation(observedRefAllele, ref.getBase(), rsIDs);
                     break;
                 case REF:
-                    vc.validateReferenceBases(observedRefAllele);
+                    vc.validateReferenceBases(observedRefAllele, ref.getBase());
                     break;
                 case IDS:
                     vc.validateRSIDs(rsIDs);

public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCF.java

@@ -71,6 +71,9 @@ public class VariantsToVCF extends RodWalker<Integer, Integer> {
     @Argument(fullName="sample", shortName="sample", doc="The sample name represented by the variant rod (for data like GELI with genotypes)", required=false)
     protected String sampleName = null;
 
+    @Argument(fullName="fixRef", shortName="fixRef", doc="Fix common reference base in case there's an indel without padding", required=false)
+    protected boolean fixReferenceBase = false;
+
     private Set<String> allowedGenotypeFormatStrings = new HashSet<String>();
     private boolean wroteHeader = false;
 
@@ -109,8 +112,11 @@ public class VariantsToVCF extends RodWalker<Integer, Integer> {
                     vc = VariantContext.modifyGenotypes(vc, genotypes);
                 }
 
-                writeRecord(vc, tracker, ref.getBase());
+            // todo - fix me. This may not be the cleanest way to handle features what need correct indel padding
+            if (fixReferenceBase) {
+                vc = new VariantContext("Variant",vc.getChr(),vc.getStart(), vc.getEnd(), vc.getAlleles(), vc.getGenotypes(), vc.getNegLog10PError(), vc.getFilters(),vc.getAttributes(), ref.getBase());
             }
+            writeRecord(vc, tracker, ref.getBase());
         }
 
         return 1;

public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java

@@ -1055,11 +1055,12 @@ public class VariantContext implements Feature { // to enable tribble intergrati
      * Run all extra-strict validation tests on a Variant Context object
      *
      * @param reference        the true reference allele
+     * @param paddedRefBase    the reference base used for padding indels
      * @param rsIDs            the true dbSNP IDs
      */
-    public void extraStrictValidation(Allele reference, Set<String> rsIDs) {
+    public void extraStrictValidation(Allele reference, Byte paddedRefBase, Set<String> rsIDs) {
         // validate the reference
-        validateReferenceBases(reference);
+        validateReferenceBases(reference, paddedRefBase);
 
         // validate the RS IDs
         validateRSIDs(rsIDs);
@@ -1074,11 +1075,15 @@ public class VariantContext implements Feature { // to enable tribble intergrati
         //checkReferenceTrack();
     }
 
-    public void validateReferenceBases(Allele reference) {
+    public void validateReferenceBases(Allele reference, Byte paddedRefBase) {
         // don't validate if we're an insertion
         if ( !reference.isNull() && !reference.basesMatch(getReference()) ) {
             throw new TribbleException.InternalCodecException(String.format("the REF allele is incorrect for the record at position %s:%d, %s vs. %s", getChr(), getStart(), reference.getBaseString(), getReference().getBaseString()));
         }
+
+        // we also need to validate the padding base for simple indels
+        if ( hasReferenceBaseForIndel() && !getReferenceBaseForIndel().equals(paddedRefBase) )
+            throw new TribbleException.InternalCodecException(String.format("the padded REF base is incorrect for the record at position %s:%d, %s vs. %s", getChr(), getStart(), (char)getReferenceBaseForIndel().byteValue(), (char)paddedRefBase.byteValue()));
     }
 
     public void validateRSIDs(Set<String> rsIDs) {